comparison test-data/files/align.log.2 @ 0:9a3a2e04f47a draft default tip

Uploaded

0:9a3a2e04f47a

inputfile = orig
3 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 3 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 3
done.

Progressive alignment ... 

STEP     1 /2 (thread    0) 
Reallocating (by thread 0) ..done. *alloclen = 1142

STEP     2 /2 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 3
Segment   1/  1    1-  84
001-0000-0 (thread    1) identical     
001-0000-0 (thread    1) better     

001-0001-1 (thread    1) identical     

001-0002-1 (thread    1) identical     
001-0002-1 (thread    1) worse      

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.